Burnin for clmm

seed

Seed for clmm

verbose

Prints progress to the screen

Details

Kang et al. (2008):

By finding the decomposition: \mathbf{G = UDU'} and premultiplying the model equation by \mathbf{U'} we get:

\mathbf{U'y = U'Xb + U'a + U'e}

with:

Var(\mathbf{U'y}) = \mathbf{U'G'U} σ^2_a + \mathbf{U'U} σ^2_e

\mathbf{U'UDU'U}σ^2_a + \mathbf{I}σ^2_e

\mathbf{D}σ^2_a + \mathbf{I}σ^2_e

After diagonalization of the variance-covariance structure the transformed model is being fitted by passing \mathbf{D}^{1/2}
as the design matrix for the random effects to clmm.
The results are subsequently backtransformed and returned by the function.